Starting phenix.real_space_refine on Thu Mar 21 01:56:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rec_19082/03_2024/8rec_19082.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rec_19082/03_2024/8rec_19082.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rec_19082/03_2024/8rec_19082.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rec_19082/03_2024/8rec_19082.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rec_19082/03_2024/8rec_19082.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rec_19082/03_2024/8rec_19082.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 104 5.49 5 Mg 1 5.21 5 S 101 5.16 5 C 17842 2.51 5 N 5131 2.21 5 O 5784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 259": "OD1" <-> "OD2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B GLU 214": "OE1" <-> "OE2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 541": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 588": "OE1" <-> "OE2" Residue "C GLU 849": "OE1" <-> "OE2" Residue "C GLU 859": "OE1" <-> "OE2" Residue "C GLU 867": "OE1" <-> "OE2" Residue "C ASP 930": "OD1" <-> "OD2" Residue "C ASP 937": "OD1" <-> "OD2" Residue "C GLU 949": "OE1" <-> "OE2" Residue "C GLU 963": "OE1" <-> "OE2" Residue "C PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 177": "OD1" <-> "OD2" Residue "D ASP 284": "OD1" <-> "OD2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 652": "OE1" <-> "OE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 663": "OE1" <-> "OE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D GLU 1187": "OE1" <-> "OE2" Residue "D GLU 1215": "OE1" <-> "OE2" Residue "D GLU 1236": "OE1" <-> "OE2" Residue "D ASP 1250": "OD1" <-> "OD2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "M GLU 159": "OE1" <-> "OE2" Residue "M ASP 160": "OD1" <-> "OD2" Residue "M ASP 292": "OD1" <-> "OD2" Residue "M PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 356": "OE1" <-> "OE2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "M TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28965 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 934 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "R" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 151 Classifications: {'RNA': 7} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna3p': 6} Chain: "T" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1053 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9654 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 721 Unresolved non-hydrogen angles: 878 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 10, 'GLU:plan': 31, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 462 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2444 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 15, 'TRANS': 331} Chain breaks: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 12, 'ASP:plan': 12} Unresolved non-hydrogen planarities: 170 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16813 SG CYS D 70 103.988 112.897 92.800 1.00 53.34 S ATOM 16942 SG CYS D 88 102.502 113.956 95.648 1.00 55.08 S ATOM 23055 SG CYS D 898 95.785 46.619 85.899 1.00 31.02 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.66 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.66 Time building chain proxies: 14.14, per 1000 atoms: 0.49 Number of scatterers: 28965 At special positions: 0 Unit cell: (142.04, 170.66, 164.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 101 16.00 P 104 15.00 Mg 1 11.99 O 5784 8.00 N 5131 7.00 C 17842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.94 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6742 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 43 sheets defined 39.7% alpha, 13.9% beta 39 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 9.88 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.911A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.713A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.191A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.747A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.560A pdb=" N LEU A 290 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.501A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.652A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.757A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 4.360A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.565A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.784A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.650A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.678A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.942A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.903A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.270A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.689A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 545 through 549 Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.748A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 608 through 612' Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.724A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.979A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.584A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.509A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.827A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.098A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.042A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.610A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 4.068A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.632A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 3.987A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 removed outlier: 3.755A pdb=" N ARG D 98 " --> pdb=" O THR D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 118 removed outlier: 3.534A pdb=" N LYS D 118 " --> pdb=" O ILE D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.899A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.202A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.797A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 640 through 644 removed outlier: 4.065A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.025A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.777A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.604A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.585A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.624A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.619A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1244 removed outlier: 3.565A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 4.016A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.726A pdb=" N VAL D1298 " --> pdb=" O ASN D1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1315 removed outlier: 3.938A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.691A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.912A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.300A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.645A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.692A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 removed outlier: 3.555A pdb=" N GLN E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.560A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.685A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.556A pdb=" N ARG M 184 " --> pdb=" O LYS M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 removed outlier: 4.158A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 4.319A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 232 through 239 removed outlier: 3.760A pdb=" N MET M 236 " --> pdb=" O PHE M 232 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.686A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 261 through 265 removed outlier: 3.642A pdb=" N ILE M 264 " --> pdb=" O GLY M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 351 Processing helix chain 'M' and resid 351 through 356 Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.596A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 384 removed outlier: 3.960A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 464 removed outlier: 4.204A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 6.575A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 111 removed outlier: 3.626A pdb=" N GLY A 106 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ALA A 138 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY A 108 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 9.500A pdb=" N GLU A 136 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 12.090A pdb=" N VAL A 110 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N THR A 134 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'B' and resid 15 through 19 removed outlier: 5.396A pdb=" N LYS B 25 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET B 205 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR B 27 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE B 203 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLU B 29 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU B 201 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 61 removed outlier: 3.834A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.556A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.873A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.873A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS C 99 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB2, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB3, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB4, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB5, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.072A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.781A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB8, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AB9, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.533A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 723 through 727 removed outlier: 5.338A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 798 through 804 removed outlier: 8.582A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.487A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS C1057 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N SER C 925 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 841 Processing sheet with id=AC8, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC9, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.782A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1340 removed outlier: 3.798A pdb=" N GLU C1340 " --> pdb=" O ALA D 19 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ALA D 19 " --> pdb=" O GLU C1340 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.693A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 111 removed outlier: 8.377A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.691A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD8, first strand: chain 'D' and resid 809 through 811 removed outlier: 6.110A pdb=" N VAL D 894 " --> pdb=" O VAL D 809 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU D 811 " --> pdb=" O VAL D 894 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.840A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 957 through 958 Processing sheet with id=AE3, first strand: chain 'D' and resid 1002 through 1003 Processing sheet with id=AE4, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.818A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 4.652A pdb=" N VAL D1176 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU D1188 " --> pdb=" O VAL D1176 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE7, first strand: chain 'M' and resid 277 through 278 removed outlier: 7.276A pdb=" N LEU M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 1128 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 14.64 Time building geometry restraints manager: 12.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.15: 1 1.15 - 1.32: 4871 1.32 - 1.48: 11810 1.48 - 1.65: 12738 1.65 - 1.81: 176 Bond restraints: 29596 Sorted by residual: bond pdb=" CB PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 1.492 0.987 0.505 5.00e-02 4.00e+02 1.02e+02 bond pdb=" CG PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 1.503 1.213 0.290 3.40e-02 8.65e+02 7.29e+01 bond pdb=" CG PRO M 211 " pdb=" CD PRO M 211 " ideal model delta sigma weight residual 1.503 1.215 0.288 3.40e-02 8.65e+02 7.15e+01 bond pdb=" N PRO M 211 " pdb=" CD PRO M 211 " ideal model delta sigma weight residual 1.473 1.552 -0.079 1.40e-02 5.10e+03 3.16e+01 bond pdb=" N PRO M 211 " pdb=" CA PRO M 211 " ideal model delta sigma weight residual 1.469 1.419 0.050 1.25e-02 6.40e+03 1.58e+01 ... (remaining 29591 not shown) Histogram of bond angle deviations from ideal: 72.68 - 94.13: 5 94.13 - 115.58: 19944 115.58 - 137.03: 20690 137.03 - 158.48: 0 158.48 - 179.93: 1 Bond angle restraints: 40640 Sorted by residual: angle pdb=" CB PRO M 258 " pdb=" CG PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 106.10 179.93 -73.83 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO M 258 " pdb=" CD PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 103.20 75.94 27.26 1.50e+00 4.44e-01 3.30e+02 angle pdb=" CA PRO M 258 " pdb=" CB PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 104.50 72.68 31.82 1.90e+00 2.77e-01 2.80e+02 angle pdb=" CA PRO M 211 " pdb=" N PRO M 211 " pdb=" CD PRO M 211 " ideal model delta sigma weight residual 112.00 93.76 18.24 1.40e+00 5.10e-01 1.70e+02 angle pdb=" N PRO M 211 " pdb=" CD PRO M 211 " pdb=" CG PRO M 211 " ideal model delta sigma weight residual 103.20 89.59 13.61 1.50e+00 4.44e-01 8.23e+01 ... (remaining 40635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 16872 35.43 - 70.86: 874 70.86 - 106.28: 38 106.28 - 141.71: 0 141.71 - 177.14: 2 Dihedral angle restraints: 17786 sinusoidal: 7336 harmonic: 10450 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 141.98 38.02 0 5.00e+00 4.00e-02 5.78e+01 dihedral pdb=" C4' DT N 6 " pdb=" C3' DT N 6 " pdb=" O3' DT N 6 " pdb=" P DC N 7 " ideal model delta sinusoidal sigma weight residual 220.00 42.86 177.14 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT N 2 " pdb=" C3' DT N 2 " pdb=" O3' DT N 2 " pdb=" P DA N 3 " ideal model delta sinusoidal sigma weight residual -140.00 19.65 -159.65 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 17783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4243 0.064 - 0.128: 557 0.128 - 0.191: 19 0.191 - 0.255: 3 0.255 - 0.319: 1 Chirality restraints: 4823 Sorted by residual: chirality pdb=" CA PRO M 211 " pdb=" N PRO M 211 " pdb=" C PRO M 211 " pdb=" CB PRO M 211 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CG LEU C 845 " pdb=" CB LEU C 845 " pdb=" CD1 LEU C 845 " pdb=" CD2 LEU C 845 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1' G R -1 " pdb=" O4' G R -1 " pdb=" C2' G R -1 " pdb=" N9 G R -1 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4820 not shown) Planarity restraints: 4964 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR M 210 " 0.094 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO M 211 " -0.216 5.00e-02 4.00e+02 pdb=" CA PRO M 211 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO M 211 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO M 468 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO M 469 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO M 469 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO M 469 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 854 " 0.052 5.00e-02 4.00e+02 7.90e-02 9.99e+00 pdb=" N PRO C 855 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 855 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO C 855 " 0.043 5.00e-02 4.00e+02 ... (remaining 4961 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 229 2.59 - 3.17: 24141 3.17 - 3.74: 45740 3.74 - 4.32: 59932 4.32 - 4.90: 99498 Nonbonded interactions: 229540 Sorted by model distance: nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.010 2.170 nonbonded pdb=" O3' A R 5 " pdb="MG MG D1501 " model vdw 2.049 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.057 2.170 nonbonded pdb=" O LEU D 71 " pdb="ZN ZN D1502 " model vdw 2.140 2.230 nonbonded pdb=" OG SER C 4 " pdb=" OE1 GLU C 7 " model vdw 2.150 2.440 ... (remaining 229535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.280 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 90.750 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.505 29596 Z= 0.333 Angle : 0.766 73.826 40640 Z= 0.383 Chirality : 0.042 0.319 4823 Planarity : 0.005 0.125 4964 Dihedral : 19.110 177.140 11044 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.82 % Favored : 94.15 % Rotamer: Outliers : 0.37 % Allowed : 28.28 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3609 helix: 1.00 (0.15), residues: 1254 sheet: 0.17 (0.26), residues: 391 loop : -1.47 (0.13), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 183 HIS 0.012 0.001 HIS M 391 PHE 0.014 0.001 PHE A 231 TYR 0.017 0.001 TYR A 185 ARG 0.008 0.000 ARG D1140 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 327 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 264 ASP cc_start: 0.6729 (p0) cc_final: 0.6153 (p0) REVERT: M 365 MET cc_start: 0.6177 (tpp) cc_final: 0.5617 (tpp) REVERT: M 376 MET cc_start: -0.1022 (tpt) cc_final: -0.1361 (tpt) outliers start: 10 outliers final: 6 residues processed: 332 average time/residue: 0.4068 time to fit residues: 212.6994 Evaluate side-chains 226 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 220 time to evaluate : 3.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 562 GLU Chi-restraints excluded: chain C residue 1164 PHE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 391 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 30.0000 chunk 280 optimal weight: 0.0670 chunk 155 optimal weight: 2.9990 chunk 95 optimal weight: 0.0000 chunk 189 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 290 optimal weight: 50.0000 chunk 112 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 336 optimal weight: 50.0000 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN B 147 GLN C 620 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN D1259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29596 Z= 0.162 Angle : 0.568 10.165 40640 Z= 0.293 Chirality : 0.041 0.214 4823 Planarity : 0.004 0.075 4964 Dihedral : 16.268 176.743 5086 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 3.65 % Allowed : 26.38 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3609 helix: 1.15 (0.15), residues: 1290 sheet: 0.20 (0.27), residues: 382 loop : -1.41 (0.14), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 183 HIS 0.003 0.001 HIS D1023 PHE 0.012 0.001 PHE C 514 TYR 0.026 0.001 TYR C 105 ARG 0.006 0.000 ARG D 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 246 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 199 ASP cc_start: 0.6376 (m-30) cc_final: 0.6134 (m-30) REVERT: C 493 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6208 (tt) REVERT: C 1085 MET cc_start: 0.8082 (mmm) cc_final: 0.7797 (mmm) REVERT: D 826 ILE cc_start: 0.7120 (OUTLIER) cc_final: 0.6891 (pt) REVERT: M 365 MET cc_start: 0.5709 (tpp) cc_final: 0.5331 (tpp) REVERT: M 376 MET cc_start: -0.0722 (tpt) cc_final: -0.1137 (tpt) REVERT: M 426 LYS cc_start: 0.7874 (mppt) cc_final: 0.7585 (pttt) REVERT: M 460 LYS cc_start: 0.6523 (pttm) cc_final: 0.5922 (ptpt) outliers start: 98 outliers final: 37 residues processed: 321 average time/residue: 0.3816 time to fit residues: 202.3259 Evaluate side-chains 251 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 212 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 975 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 391 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 10.0000 chunk 104 optimal weight: 0.2980 chunk 279 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 92 optimal weight: 50.0000 chunk 336 optimal weight: 0.1980 chunk 363 optimal weight: 40.0000 chunk 299 optimal weight: 0.4980 chunk 333 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 270 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29596 Z= 0.147 Angle : 0.535 8.233 40640 Z= 0.275 Chirality : 0.040 0.222 4823 Planarity : 0.004 0.063 4964 Dihedral : 16.178 177.226 5078 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 3.06 % Allowed : 27.16 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3609 helix: 1.28 (0.15), residues: 1302 sheet: 0.43 (0.27), residues: 382 loop : -1.41 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 183 HIS 0.007 0.001 HIS M 406 PHE 0.010 0.001 PHE C 514 TYR 0.017 0.001 TYR A 185 ARG 0.009 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 236 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 796 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7716 (pp) REVERT: C 1085 MET cc_start: 0.7983 (mmm) cc_final: 0.7199 (mmm) REVERT: D 826 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6878 (pt) REVERT: E 62 GLN cc_start: 0.7685 (tp40) cc_final: 0.7443 (tp40) REVERT: M 365 MET cc_start: 0.5681 (tpp) cc_final: 0.5436 (tpp) REVERT: M 376 MET cc_start: -0.0781 (tpt) cc_final: -0.1222 (tpt) REVERT: M 460 LYS cc_start: 0.6511 (pttm) cc_final: 0.5549 (ptpt) outliers start: 82 outliers final: 43 residues processed: 298 average time/residue: 0.3718 time to fit residues: 182.8599 Evaluate side-chains 255 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 210 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 391 HIS Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 0.2980 chunk 253 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 160 optimal weight: 40.0000 chunk 226 optimal weight: 10.0000 chunk 337 optimal weight: 0.0770 chunk 357 optimal weight: 7.9990 chunk 176 optimal weight: 9.9990 chunk 320 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 overall best weight: 2.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1009 ASN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29596 Z= 0.174 Angle : 0.533 10.206 40640 Z= 0.273 Chirality : 0.040 0.220 4823 Planarity : 0.004 0.076 4964 Dihedral : 16.141 177.587 5078 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 3.65 % Allowed : 26.53 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3609 helix: 1.42 (0.15), residues: 1309 sheet: 0.38 (0.27), residues: 376 loop : -1.38 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 115 HIS 0.005 0.001 HIS M 406 PHE 0.009 0.001 PHE M 397 TYR 0.019 0.001 TYR A 185 ARG 0.012 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 217 time to evaluate : 3.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 ASP cc_start: 0.5902 (p0) cc_final: 0.5581 (p0) REVERT: C 796 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7807 (pp) REVERT: C 1085 MET cc_start: 0.7999 (mmm) cc_final: 0.7286 (mmm) REVERT: C 1107 MET cc_start: 0.7608 (mpp) cc_final: 0.7308 (mpp) REVERT: D 826 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6986 (pt) REVERT: M 376 MET cc_start: -0.1187 (tpt) cc_final: -0.1497 (tpt) REVERT: M 460 LYS cc_start: 0.6549 (pttm) cc_final: 0.5592 (ptpt) outliers start: 98 outliers final: 58 residues processed: 295 average time/residue: 0.3568 time to fit residues: 177.5742 Evaluate side-chains 265 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 205 time to evaluate : 3.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 266 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 chunk 305 optimal weight: 3.9990 chunk 247 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 182 optimal weight: 0.9990 chunk 321 optimal weight: 9.9990 chunk 90 optimal weight: 0.0270 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29596 Z= 0.149 Angle : 0.525 10.747 40640 Z= 0.268 Chirality : 0.040 0.214 4823 Planarity : 0.004 0.068 4964 Dihedral : 16.128 177.969 5076 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.57 % Rotamer: Outliers : 3.50 % Allowed : 26.34 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3609 helix: 1.52 (0.15), residues: 1304 sheet: 0.46 (0.27), residues: 374 loop : -1.35 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 212 HIS 0.004 0.001 HIS M 406 PHE 0.009 0.001 PHE C 514 TYR 0.016 0.001 TYR A 185 ARG 0.013 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 219 time to evaluate : 3.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 796 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7773 (pp) REVERT: C 1085 MET cc_start: 0.8028 (mmm) cc_final: 0.7387 (mmm) REVERT: C 1107 MET cc_start: 0.7615 (mpp) cc_final: 0.7374 (mpp) REVERT: D 558 ASP cc_start: 0.6029 (p0) cc_final: 0.5824 (p0) REVERT: D 826 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6954 (pt) REVERT: E 62 GLN cc_start: 0.7828 (tp40) cc_final: 0.7566 (tp40) REVERT: M 376 MET cc_start: -0.1227 (tpt) cc_final: -0.1741 (tpt) REVERT: M 426 LYS cc_start: 0.7765 (pttt) cc_final: 0.7476 (ptpt) REVERT: M 460 LYS cc_start: 0.6368 (pttm) cc_final: 0.5402 (ptpt) outliers start: 94 outliers final: 62 residues processed: 293 average time/residue: 0.3645 time to fit residues: 178.1217 Evaluate side-chains 270 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 206 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1241 TYR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 6.9990 chunk 322 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 88 optimal weight: 0.0970 chunk 357 optimal weight: 8.9990 chunk 297 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 187 optimal weight: 0.0370 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29596 Z= 0.137 Angle : 0.524 10.555 40640 Z= 0.266 Chirality : 0.039 0.230 4823 Planarity : 0.004 0.061 4964 Dihedral : 16.109 178.399 5076 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 3.32 % Allowed : 26.60 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3609 helix: 1.57 (0.15), residues: 1305 sheet: 0.63 (0.27), residues: 386 loop : -1.35 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 212 HIS 0.004 0.000 HIS M 406 PHE 0.010 0.001 PHE C 545 TYR 0.019 0.001 TYR A 185 ARG 0.015 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 222 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 796 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7732 (pp) REVERT: C 1085 MET cc_start: 0.8001 (mmm) cc_final: 0.7292 (mmm) REVERT: C 1107 MET cc_start: 0.7632 (mpp) cc_final: 0.7366 (mpp) REVERT: D 826 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.7019 (pt) REVERT: M 376 MET cc_start: -0.0916 (tpt) cc_final: -0.1225 (tpt) REVERT: M 426 LYS cc_start: 0.7666 (pttt) cc_final: 0.7392 (ptpt) REVERT: M 460 LYS cc_start: 0.6169 (pttm) cc_final: 0.5235 (ptpt) outliers start: 89 outliers final: 62 residues processed: 293 average time/residue: 0.3684 time to fit residues: 179.2541 Evaluate side-chains 270 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 206 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1241 TYR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 206 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 0.5980 chunk 40 optimal weight: 8.9990 chunk 203 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 301 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 356 optimal weight: 40.0000 chunk 223 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29596 Z= 0.170 Angle : 0.540 12.853 40640 Z= 0.273 Chirality : 0.040 0.334 4823 Planarity : 0.004 0.062 4964 Dihedral : 16.087 173.784 5076 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 3.46 % Allowed : 26.60 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3609 helix: 1.67 (0.15), residues: 1304 sheet: 0.64 (0.27), residues: 394 loop : -1.31 (0.14), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 212 HIS 0.005 0.001 HIS M 406 PHE 0.011 0.001 PHE C 545 TYR 0.018 0.001 TYR A 185 ARG 0.016 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 204 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 796 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7752 (pp) REVERT: C 1085 MET cc_start: 0.8005 (mmm) cc_final: 0.7321 (mmm) REVERT: C 1107 MET cc_start: 0.7534 (mpp) cc_final: 0.7304 (mpp) REVERT: D 826 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.7059 (pt) REVERT: M 376 MET cc_start: -0.0491 (tpt) cc_final: -0.0773 (tpt) REVERT: M 460 LYS cc_start: 0.6166 (pttm) cc_final: 0.5238 (ptpt) outliers start: 93 outliers final: 70 residues processed: 278 average time/residue: 0.3571 time to fit residues: 167.2154 Evaluate side-chains 272 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 200 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 0.0470 chunk 142 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 69 optimal weight: 0.0030 chunk 226 optimal weight: 0.0170 chunk 242 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 280 optimal weight: 20.0000 overall best weight: 0.9928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29596 Z= 0.141 Angle : 0.537 13.778 40640 Z= 0.271 Chirality : 0.040 0.207 4823 Planarity : 0.004 0.054 4964 Dihedral : 16.083 175.828 5076 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.40 % Favored : 94.54 % Rotamer: Outliers : 3.02 % Allowed : 26.79 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3609 helix: 1.65 (0.15), residues: 1305 sheet: 0.62 (0.27), residues: 374 loop : -1.29 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 212 HIS 0.003 0.000 HIS M 406 PHE 0.010 0.001 PHE C 545 TYR 0.017 0.001 TYR A 185 ARG 0.017 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 215 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 796 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7878 (pp) REVERT: C 1085 MET cc_start: 0.7983 (mmm) cc_final: 0.7247 (mmm) REVERT: C 1107 MET cc_start: 0.7578 (mpp) cc_final: 0.7321 (mpp) REVERT: D 826 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.7017 (pt) REVERT: M 460 LYS cc_start: 0.6163 (pttm) cc_final: 0.5237 (ptpt) outliers start: 81 outliers final: 64 residues processed: 281 average time/residue: 0.3563 time to fit residues: 169.5561 Evaluate side-chains 267 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 201 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1136 GLN Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 206 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 5.9990 chunk 341 optimal weight: 9.9990 chunk 311 optimal weight: 20.0000 chunk 332 optimal weight: 0.0010 chunk 200 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 260 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 300 optimal weight: 50.0000 chunk 314 optimal weight: 10.0000 chunk 331 optimal weight: 1.9990 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29596 Z= 0.236 Angle : 0.572 15.349 40640 Z= 0.290 Chirality : 0.041 0.301 4823 Planarity : 0.004 0.059 4964 Dihedral : 16.092 176.933 5076 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.01 % Rotamer: Outliers : 2.91 % Allowed : 26.86 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3609 helix: 1.74 (0.15), residues: 1303 sheet: 0.56 (0.27), residues: 388 loop : -1.26 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP M 212 HIS 0.003 0.001 HIS M 406 PHE 0.010 0.001 PHE M 397 TYR 0.020 0.001 TYR M 112 ARG 0.010 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 199 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 796 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8047 (pp) REVERT: C 1069 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.8152 (ptt180) REVERT: C 1085 MET cc_start: 0.8068 (mmm) cc_final: 0.7251 (mmm) REVERT: C 1107 MET cc_start: 0.7519 (mpp) cc_final: 0.7004 (mpp) REVERT: D 558 ASP cc_start: 0.6388 (p0) cc_final: 0.6176 (p0) REVERT: D 826 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7138 (pt) REVERT: M 460 LYS cc_start: 0.6251 (pttm) cc_final: 0.5335 (ptpt) outliers start: 78 outliers final: 63 residues processed: 263 average time/residue: 0.3717 time to fit residues: 162.6789 Evaluate side-chains 253 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 187 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 5.9990 chunk 351 optimal weight: 0.0570 chunk 214 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 368 optimal weight: 40.0000 chunk 339 optimal weight: 0.7980 chunk 293 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 overall best weight: 3.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29596 Z= 0.221 Angle : 0.577 15.341 40640 Z= 0.291 Chirality : 0.041 0.351 4823 Planarity : 0.004 0.058 4964 Dihedral : 16.099 177.374 5076 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.76 % Favored : 94.18 % Rotamer: Outliers : 2.76 % Allowed : 26.94 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3609 helix: 1.68 (0.15), residues: 1304 sheet: 0.56 (0.27), residues: 388 loop : -1.25 (0.14), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 212 HIS 0.003 0.001 HIS D 865 PHE 0.009 0.001 PHE C1323 TYR 0.018 0.001 TYR A 185 ARG 0.016 0.000 ARG E 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7218 Ramachandran restraints generated. 3609 Oldfield, 0 Emsley, 3609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 196 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 796 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8035 (pp) REVERT: C 1085 MET cc_start: 0.8045 (mmm) cc_final: 0.7225 (mmm) REVERT: C 1107 MET cc_start: 0.7555 (mpp) cc_final: 0.7304 (mpp) REVERT: D 826 ILE cc_start: 0.7447 (OUTLIER) cc_final: 0.7225 (pt) REVERT: M 460 LYS cc_start: 0.6243 (pttm) cc_final: 0.5321 (ptpt) outliers start: 74 outliers final: 64 residues processed: 254 average time/residue: 0.3751 time to fit residues: 159.1900 Evaluate side-chains 256 residues out of total 3111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 190 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 103 ASN Chi-restraints excluded: chain A residue 104 LYS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 403 MET Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 547 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1075 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1226 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1298 VAL Chi-restraints excluded: chain C residue 1322 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 571 ASP Chi-restraints excluded: chain D residue 601 ILE Chi-restraints excluded: chain D residue 604 MET Chi-restraints excluded: chain D residue 699 ASP Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 737 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain M residue 206 PHE Chi-restraints excluded: chain M residue 248 GLU Chi-restraints excluded: chain M residue 401 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 1.9990 chunk 312 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 270 optimal weight: 0.1980 chunk 43 optimal weight: 0.3980 chunk 81 optimal weight: 10.0000 chunk 293 optimal weight: 50.0000 chunk 123 optimal weight: 5.9990 chunk 301 optimal weight: 50.0000 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.088179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.057451 restraints weight = 97364.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.059388 restraints weight = 45986.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.060593 restraints weight = 29190.714| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29596 Z= 0.171 Angle : 0.571 14.559 40640 Z= 0.287 Chirality : 0.040 0.203 4823 Planarity : 0.004 0.091 4964 Dihedral : 16.076 177.252 5075 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 2.72 % Allowed : 26.97 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3609 helix: 1.68 (0.15), residues: 1307 sheet: 0.63 (0.27), residues: 393 loop : -1.26 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 212 HIS 0.003 0.001 HIS M 406 PHE 0.012 0.001 PHE C 545 TYR 0.030 0.001 TYR M 112 ARG 0.020 0.000 ARG E 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5049.48 seconds wall clock time: 92 minutes 39.41 seconds (5559.41 seconds total)